Objective: To compare the differences in composition and function of gut microbiota between patients with chronic spontaneous urticaria and healthy individuals, and to explore the correlation between gut microbiota and the pathogenesis of chronic spontaneous urticaria. Methods: A total of 15 CSU patients and 15 healthy controls were enrolled. Fecal samples were collected for total DNA extraction, metagenomic sequencing and subsequent bioinformatic analysis. The differences in species composition, diversity and functional pathways of gut microbiota were compared between the two groups. Results: There was no significant difference in Alpha diversity indices between the two groups (P > 0.05), while a significant difference was observed in Beta diversity (P < 0.05). Species revealed showed that the relative abundance of Bifidobacterium was increased in the CSU group. By contrast, the abundances of Bacteroidetes, Bacteroides and Faecalibacterium prausnitzii were decreased in CSU patients (P < 0.05). A total of 42 differentially expressed functional pathways were identified via functional annotation. Pathways including lipopolysaccharide biosynthesis and one-carbon pool by folate were enriched in the CSU group, whereas starch and sucrose metabolism as well as galactose metabolism were enriched in healthy controls (P < 0.05). Conclusion: Patients with CSU present obvious gut microbiota dysbiosis and aberrant metabolic pathways. Such alterations may be associated with the pathogenesis of CSU.